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- PDB-8i9m: The RAGE and HMGB1 complex -

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Basic information

Entry
Database: PDB / ID: 8i9m
TitleThe RAGE and HMGB1 complex
Components
  • Advanced glycosylation end product-specific receptor
  • High mobility group protein B1
KeywordsIMMUNE SYSTEM / RAGE / HMGB1 / Inflammation
Function / homology
Function and homology information


: / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / advanced glycation end-product receptor activity / negative regulation of blood circulation / positive regulation of endothelin production / regulation of CD4-positive, alpha-beta T cell activation ...: / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / advanced glycation end-product receptor activity / negative regulation of blood circulation / positive regulation of endothelin production / regulation of CD4-positive, alpha-beta T cell activation / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation / glucose mediated signaling pathway / T-helper 1 cell activation / positive regulation of monocyte extravasation / regulation of T cell mediated cytotoxicity / T-helper 1 cell differentiation / positive regulation of DNA-templated DNA replication / positive regulation of myeloid cell differentiation / positive regulation of toll-like receptor 2 signaling pathway / negative regulation of long-term synaptic depression / positive regulation of dendritic cell differentiation / regulation of p38MAPK cascade / C-X-C chemokine binding / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / regulation of non-canonical NF-kappaB signal transduction / positive regulation of amyloid precursor protein catabolic process / positive regulation of glycogen catabolic process / DNA geometric change / positive regulation of toll-like receptor 4 signaling pathway / endothelial cell chemotaxis / transcytosis / RAGE receptor binding / eye development / positive regulation of interleukin-1 production / Regulation of TLR by endogenous ligand / bubble DNA binding / induction of positive chemotaxis / V(D)J recombination / myeloid cell differentiation / alphav-beta3 integrin-HMGB1 complex / Apoptosis induced DNA fragmentation / myeloid progenitor cell differentiation / inflammatory response to antigenic stimulus / macrophage activation involved in immune response / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / regulation of nucleotide-excision repair / positive regulation of monocyte chemotactic protein-1 production / S100 protein binding / positive regulation of p38MAPK cascade / regulation of long-term synaptic potentiation / cellular response to interleukin-7 / endothelial cell proliferation / positive regulation of chemokine (C-X-C motif) ligand 2 production / protein localization to membrane / glycogen catabolic process / apoptotic cell clearance / supercoiled DNA binding / regulation of spontaneous synaptic transmission / positive regulation of vascular endothelial cell proliferation / negative regulation of connective tissue replacement involved in inflammatory response wound healing / DNA binding, bending / IRAK4 deficiency (TLR2/4) / dendritic cell chemotaxis / scavenger receptor activity / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of DNA binding / laminin receptor activity / positive regulation of wound healing / phosphatidylserine binding / negative regulation of interleukin-10 production / positive regulation of double-strand break repair / positive regulation of sprouting angiogenesis / chemoattractant activity / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of activated T cell proliferation / response to amyloid-beta / TRAF6 mediated NF-kB activation / negative regulation of type II interferon production / DNA topological change / Advanced glycosylation endproduct receptor signaling / positive regulation of interferon-alpha production / negative regulation of long-term synaptic potentiation / positive regulation of interleukin-10 production / negative regulation of blood vessel endothelial cell migration / protein kinase activator activity / positive regulation of blood vessel endothelial cell migration / Pyroptosis / phagocytosis / phagocytic cup / transport across blood-brain barrier / positive regulation of chemokine production / four-way junction DNA binding / condensed chromosome
Similarity search - Function
: / HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / HMG-box domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group ...: / HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / HMG-box domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
High mobility group protein B1 / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.19 Å
AuthorsHan, C.W. / Kim, H.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The RAGE and HMGB1 complex
Authors: Han, C.W. / Kim, H.J.
History
DepositionFeb 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: High mobility group protein B1
B: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)31,6592
Polymers31,6592
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, 1 copy of chain A 1 copy of chain B
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein High mobility group protein B1 / High mobility group protein 1 / HMG-1


Mass: 8590.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMGB1, HMG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09429
#2: Protein Advanced glycosylation end product-specific receptor / Receptor for advanced glycosylation end products


Mass: 23068.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Production host: Escherichia coli (E. coli) / References: UniProt: Q15109
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The RAGE and HMGB1 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.50 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 39.99 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121467 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01452289
ELECTRON MICROSCOPYf_angle_d2.31213103
ELECTRON MICROSCOPYf_chiral_restr0.1215324
ELECTRON MICROSCOPYf_plane_restr0.0181409
ELECTRON MICROSCOPYf_dihedral_angle_d13.46551408

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